FMO DATABASE

FMODB ID: J3969

Calculation Name: 3MJK-X-Xray372

Preferred Name: Platelet-derived growth factor subunit A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3MJK

Chain ID: X

ChEMBL ID: CHEMBL3137294

UniProt ID: P04085

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-860700.901199
FMO2-HF: Nuclear repulsion	811015.309604
FMO2-HF: Total energy	-49685.591595
FMO2-MP2: Total energy	-49826.426254

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(X:23:ALA)

Summations of interaction energy for fragment #1(X:23:ALA)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-1.182	0.428	0.019	-0.632	-0.995	0.001

Interaction energy analysis for fragmet #1(X:23:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.030

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	X	25	ILE	0	-0.023	-0.014	3.062	-2.147	-0.601	0.020	-0.628	-0.937	0.001
4	X	26	PRO	0	0.075	0.044	5.083	-0.635	-0.571	-0.001	-0.004	-0.058	0.000
5	X	27	ARG	1	0.925	0.963	8.088	0.792	0.792	0.000	0.000	0.000	0.000
6	X	28	GLU	-1	-0.840	-0.918	9.622	-0.064	-0.064	0.000	0.000	0.000	0.000
7	X	29	VAL	0	0.094	0.050	8.677	0.061	0.061	0.000	0.000	0.000	0.000
8	X	30	ILE	0	0.013	0.013	5.774	0.105	0.105	0.000	0.000	0.000	0.000
9	X	31	GLU	-1	-0.864	-0.956	10.164	-0.403	-0.403	0.000	0.000	0.000	0.000
10	X	32	ARG	1	0.770	0.884	13.286	0.119	0.119	0.000	0.000	0.000	0.000
11	X	33	LEU	0	0.030	0.012	10.592	0.023	0.023	0.000	0.000	0.000	0.000
12	X	34	ALA	0	-0.045	-0.010	13.986	0.024	0.024	0.000	0.000	0.000	0.000
13	X	35	ARG	1	0.831	0.936	15.533	0.245	0.245	0.000	0.000	0.000	0.000
14	X	36	SER	0	0.000	-0.021	17.623	0.020	0.020	0.000	0.000	0.000	0.000
15	X	37	GLN	0	-0.041	-0.016	19.500	0.005	0.005	0.000	0.000	0.000	0.000
16	X	38	ILE	0	0.012	0.003	15.906	0.008	0.008	0.000	0.000	0.000	0.000
17	X	39	HIS	0	-0.044	-0.032	20.310	-0.001	-0.001	0.000	0.000	0.000	0.000
18	X	40	SER	0	-0.010	-0.014	21.901	0.005	0.005	0.000	0.000	0.000	0.000
19	X	41	ILE	0	0.026	0.001	18.334	0.001	0.001	0.000	0.000	0.000	0.000
20	X	42	ARG	1	0.893	0.928	19.698	-0.044	-0.044	0.000	0.000	0.000	0.000
21	X	43	ASP	-1	-0.877	-0.925	21.546	0.028	0.028	0.000	0.000	0.000	0.000
22	X	44	LEU	0	-0.047	-0.032	13.860	-0.009	-0.009	0.000	0.000	0.000	0.000
23	X	45	GLN	0	-0.029	-0.001	16.702	0.001	0.001	0.000	0.000	0.000	0.000
24	X	46	ARG	0	0.153	0.113	17.995	0.001	0.001	0.000	0.000	0.000	0.000
25	X	47	LEU	0	-0.055	-0.008	18.065	-0.004	-0.004	0.000	0.000	0.000	0.000
26	X	48	LEU	0	-0.088	-0.036	11.506	-0.026	-0.026	0.000	0.000	0.000	0.000
27	X	49	GLU	-1	-0.961	-0.995	15.428	0.135	0.135	0.000	0.000	0.000	0.000
28	X	88	ILE	0	0.012	0.003	26.395	0.002	0.002	0.000	0.000	0.000	0.000
29	X	89	GLU	-1	-1.001	-0.997	27.959	0.045	0.045	0.000	0.000	0.000	0.000
30	X	90	GLU	-1	-0.856	-0.927	22.812	0.084	0.084	0.000	0.000	0.000	0.000
31	X	91	ALA	0	-0.019	-0.016	21.390	-0.009	-0.009	0.000	0.000	0.000	0.000
32	X	92	VAL	0	0.054	0.025	23.030	-0.001	-0.001	0.000	0.000	0.000	0.000
33	X	93	PRO	0	0.003	0.011	20.441	-0.004	-0.004	0.000	0.000	0.000	0.000
34	X	94	ALA	0	-0.011	-0.007	22.350	-0.004	-0.004	0.000	0.000	0.000	0.000
35	X	95	VAL	0	0.054	0.012	22.685	-0.009	-0.009	0.000	0.000	0.000	0.000
36	X	96	CYS	0	0.002	0.017	19.157	0.007	0.007	0.000	0.000	0.000	0.000
37	X	97	LYS	1	0.970	0.983	24.567	0.024	0.024	0.000	0.000	0.000	0.000
38	X	98	THR	0	0.024	0.012	28.250	-0.002	-0.002	0.000	0.000	0.000	0.000
39	X	99	ARG	1	0.790	0.883	26.351	0.036	0.036	0.000	0.000	0.000	0.000
40	X	100	THR	0	-0.034	-0.031	31.954	-0.004	-0.004	0.000	0.000	0.000	0.000
41	X	101	VAL	0	-0.019	-0.002	29.740	0.002	0.002	0.000	0.000	0.000	0.000
42	X	102	ILE	0	0.033	0.003	33.153	0.000	0.000	0.000	0.000	0.000	0.000
43	X	103	TYR	0	-0.025	-0.014	34.030	-0.002	-0.002	0.000	0.000	0.000	0.000
44	X	104	GLU	-1	-0.894	-0.958	35.860	-0.019	-0.019	0.000	0.000	0.000	0.000
45	X	105	ILE	0	-0.050	-0.022	37.757	-0.003	-0.003	0.000	0.000	0.000	0.000
46	X	106	PRO	0	0.039	0.018	37.190	0.002	0.002	0.000	0.000	0.000	0.000
47	X	107	ARG	1	0.946	0.952	39.688	0.018	0.018	0.000	0.000	0.000	0.000
48	X	108	SER	0	0.047	0.024	38.937	0.001	0.001	0.000	0.000	0.000	0.000
49	X	109	GLN	0	-0.001	0.004	39.553	0.000	0.000	0.000	0.000	0.000	0.000
50	X	110	VAL	0	-0.063	-0.037	42.606	0.001	0.001	0.000	0.000	0.000	0.000
51	X	111	ASP	-1	-0.816	-0.906	45.597	-0.021	-0.021	0.000	0.000	0.000	0.000
52	X	112	PRO	0	-0.012	-0.001	43.325	0.001	0.001	0.000	0.000	0.000	0.000
53	X	113	THR	0	-0.058	-0.011	44.966	-0.001	-0.001	0.000	0.000	0.000	0.000
54	X	114	SER	0	-0.041	-0.043	47.301	0.002	0.002	0.000	0.000	0.000	0.000
55	X	115	ALA	0	0.050	0.022	45.601	-0.001	-0.001	0.000	0.000	0.000	0.000
56	X	116	ASN	0	-0.012	0.010	47.327	0.000	0.000	0.000	0.000	0.000	0.000
57	X	117	PHE	0	-0.044	-0.029	46.174	0.001	0.001	0.000	0.000	0.000	0.000
58	X	118	LEU	0	0.015	0.009	47.198	0.000	0.000	0.000	0.000	0.000	0.000
59	X	119	ILE	0	0.021	0.022	43.834	0.000	0.000	0.000	0.000	0.000	0.000
60	X	120	TRP	0	-0.013	0.022	46.788	0.000	0.000	0.000	0.000	0.000	0.000
61	X	121	PRO	0	0.060	0.016	44.963	0.000	0.000	0.000	0.000	0.000	0.000
62	X	122	PRO	0	0.017	0.002	42.513	-0.001	-0.001	0.000	0.000	0.000	0.000
63	X	123	CYS	0	-0.022	-0.012	39.029	-0.001	-0.001	0.000	0.000	0.000	0.000
64	X	124	VAL	0	-0.003	0.000	39.547	0.002	0.002	0.000	0.000	0.000	0.000
65	X	125	GLU	-1	-0.858	-0.906	37.725	-0.019	-0.019	0.000	0.000	0.000	0.000
66	X	126	VAL	0	-0.052	-0.022	34.294	-0.001	-0.001	0.000	0.000	0.000	0.000
67	X	127	LYS	1	0.940	0.978	34.267	0.026	0.026	0.000	0.000	0.000	0.000
68	X	128	ARG	1	0.889	0.934	29.691	0.046	0.046	0.000	0.000	0.000	0.000
69	X	129	CYS	0	-0.040	0.006	26.615	0.003	0.003	0.000	0.000	0.000	0.000
70	X	130	THR	0	0.024	0.013	25.319	0.000	0.000	0.000	0.000	0.000	0.000
71	X	131	GLY	0	0.027	0.013	23.332	0.003	0.003	0.000	0.000	0.000	0.000
72	X	132	CYS	0	-0.041	-0.027	17.813	-0.007	-0.007	0.000	0.000	0.000	0.000
73	X	133	CYS	0	-0.013	0.014	17.317	0.013	0.013	0.000	0.000	0.000	0.000
74	X	134	ASN	0	-0.009	-0.008	15.651	0.005	0.005	0.000	0.000	0.000	0.000
75	X	135	THR	0	0.022	0.025	11.199	0.018	0.018	0.000	0.000	0.000	0.000
76	X	136	SER	0	0.066	0.019	10.703	0.012	0.012	0.000	0.000	0.000	0.000
77	X	137	SER	0	-0.020	-0.007	10.941	-0.006	-0.006	0.000	0.000	0.000	0.000
78	X	138	VAL	0	-0.062	-0.017	12.743	0.008	0.008	0.000	0.000	0.000	0.000
79	X	139	LYS	1	0.900	0.952	16.191	0.277	0.277	0.000	0.000	0.000	0.000
80	X	141	GLN	0	0.000	-0.008	22.389	0.004	0.004	0.000	0.000	0.000	0.000
81	X	142	PRO	0	0.062	0.007	24.927	0.006	0.006	0.000	0.000	0.000	0.000
82	X	143	SER	0	-0.015	-0.021	28.729	-0.005	-0.005	0.000	0.000	0.000	0.000
83	X	144	ARG	1	0.874	0.924	30.650	0.050	0.050	0.000	0.000	0.000	0.000
84	X	145	VAL	0	-0.004	0.005	33.089	0.002	0.002	0.000	0.000	0.000	0.000
85	X	146	HIS	0	-0.008	-0.001	34.943	0.002	0.002	0.000	0.000	0.000	0.000
86	X	147	HIS	0	-0.047	-0.048	35.479	0.001	0.001	0.000	0.000	0.000	0.000
87	X	148	ARG	1	0.868	0.915	39.982	0.031	0.031	0.000	0.000	0.000	0.000
88	X	149	SER	0	-0.006	-0.011	42.847	-0.001	-0.001	0.000	0.000	0.000	0.000
89	X	150	VAL	0	-0.027	-0.006	44.236	0.001	0.001	0.000	0.000	0.000	0.000
90	X	151	LYS	1	0.860	0.906	46.785	0.016	0.016	0.000	0.000	0.000	0.000
91	X	152	VAL	0	0.002	0.017	45.332	0.001	0.001	0.000	0.000	0.000	0.000
92	X	153	ALA	0	0.007	-0.007	48.747	0.000	0.000	0.000	0.000	0.000	0.000
93	X	154	LYS	1	0.831	0.931	49.734	0.019	0.019	0.000	0.000	0.000	0.000
94	X	155	VAL	0	0.000	-0.023	51.339	0.001	0.001	0.000	0.000	0.000	0.000
95	X	156	GLU	-1	-0.766	-0.885	52.369	-0.016	-0.016	0.000	0.000	0.000	0.000
96	X	157	TYR	0	0.042	0.012	54.796	0.000	0.000	0.000	0.000	0.000	0.000
97	X	158	VAL	0	-0.008	-0.006	57.794	0.000	0.000	0.000	0.000	0.000	0.000
98	X	159	ARG	1	1.001	0.988	60.345	0.011	0.011	0.000	0.000	0.000	0.000
99	X	160	LYS	1	0.969	0.979	61.849	0.006	0.006	0.000	0.000	0.000	0.000
100	X	161	LYS	1	0.960	0.986	62.561	0.008	0.008	0.000	0.000	0.000	0.000
101	X	162	PRO	0	0.017	0.045	58.893	-0.001	-0.001	0.000	0.000	0.000	0.000
102	X	163	LYS	1	0.823	0.901	56.783	0.014	0.014	0.000	0.000	0.000	0.000
103	X	164	LEU	0	0.029	0.005	54.770	0.000	0.000	0.000	0.000	0.000	0.000
104	X	165	LYS	1	0.955	0.994	53.844	0.018	0.018	0.000	0.000	0.000	0.000
105	X	166	GLU	-1	-0.817	-0.892	52.832	-0.017	-0.017	0.000	0.000	0.000	0.000
106	X	167	VAL	0	-0.029	-0.015	48.066	0.000	0.000	0.000	0.000	0.000	0.000
107	X	168	GLN	0	0.025	0.022	47.217	0.000	0.000	0.000	0.000	0.000	0.000
108	X	169	VAL	0	0.003	-0.001	42.232	-0.001	-0.001	0.000	0.000	0.000	0.000
109	X	170	ARG	1	0.949	0.973	37.136	0.048	0.048	0.000	0.000	0.000	0.000
110	X	171	LEU	0	-0.013	0.002	39.136	-0.001	-0.001	0.000	0.000	0.000	0.000
111	X	172	GLU	-1	-0.810	-0.901	32.277	-0.062	-0.062	0.000	0.000	0.000	0.000
112	X	173	GLU	-1	-0.791	-0.860	35.246	-0.030	-0.030	0.000	0.000	0.000	0.000
113	X	174	HIS	0	0.003	-0.015	29.156	-0.002	-0.002	0.000	0.000	0.000	0.000
114	X	175	LEU	0	-0.052	-0.030	33.461	0.004	0.004	0.000	0.000	0.000	0.000
115	X	176	GLU	-1	-0.851	-0.908	31.992	-0.051	-0.051	0.000	0.000	0.000	0.000
116	X	178	ALA	0	0.031	0.019	25.664	0.004	0.004	0.000	0.000	0.000	0.000
117	X	180	ALA	0	0.030	0.023	21.093	-0.004	-0.004	0.000	0.000	0.000	0.000
118	X	181	THR	0	0.025	-0.001	16.298	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(X:23:ALA)